Data from: Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity

Cheng T, Xu C, Lei L, Li C, Zhang Y, Zhou S

Date Published: June 16, 2015

DOI: http://dx.doi.org/10.5061/dryad.p3ks4

 

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Title Alignments of 18S,5.8S and 26S rDNA sequences of plants and fungal
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Description The alignments were constructed using 18S, 5.8S and 26S rDNA sequences of all plants and fungal from GenBank on 9th February 2013. Multiple alignments of every group were conducted using MAFFT v6.864 (Katoh et al. 2005). The regions from NS7 priming site to the 3’ end of 18S, the 5’ end to LR3 priming site of 26S, and the complete 5.8S region were extracted for primer design and in silico tests. The "NonGreen plants" includes Rhodophytes and Glaucophytes. The "Basal fungi" includes Microsporidia and Cryptomycota.
Download Alignments of 18S,5.8S and 26S rDNA seque...al.zip (8.300 Mb)
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Title Perl scripts used in designing and evaluating ITS primers of plants.
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Description These perl scripts were designed by Tao Cheng in 2014 for designing and evaluating ITS primers of plants. The related article has been submitted to Molecular Ecology Resources. The descriptions of each script are as follow: Classifier_Fungi.pl Function: Divide the total Fungi sequences into lower classification level. Classifier_Viridiplantae.pl Function: Divide the total sequences into lower classification level. N_Degenerate_Filter_New.pl Function: Get rid of the sequences with 'n' or degenerate character. contaminantsFilter.pl Function: Remove the potential contaminated sequences from GenBank based on mega-blast. GenBanktoFastawithClassName.pl Function: Convert a GB file to fasta format in following style: # >Class_Genus_Species_TaxonID_GI_ACC_length description # >Nelumbonaceae_Nelumbo_lutea_4431_1479989_L75835_1713 Nelumbo lutea 18S ribosomal RNA (18S rDNA) gene # nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnncc atgcatgtgt # aagtatgaac taattcagac tgtgaaactg cgaatggctc attaaatcag ttatagtttg # tttgatggta tctactactc ggataaccgt agtaattcta gagctaatac gtgcaccaaa # ................................................................. # ttgcaattgt tggtcttcaa cgaggaattc ctagtaagcg cgagtcatca gctcgcgttg # actacgtccc tgccctttgt acacaccgcc cgtcgctcct accgattgaa tggtccggtg # aagtgttcgg atcgcggcga cgtgggcggt tcg Find_Conserved_DNA_Segments.pl Function: This script is used to extract conserved DNA segments from an alignment file. MismatchDetect-Batch.pl Function: Calculate the species coverage between the primer and every target sequence.User set the mismatch allowed and the threshold of nucleotides constrained in the 3'-end. getPCRProductLengthByPrimerBlast.pl Function: This script is used to get the PCR product length of a certain primer-pair based on PrimerBlast.
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Download Programs-ITS-primers-Tao Cheng-2014.zip (29.28 Kb)
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When using this data, please cite the original publication:

Cheng T, Xu C, Lei L, Li C, Zhang Y, Zhou S (2015) Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity. Molecular Ecology Resources 16(1):138-149. http://dx.doi.org/10.1111/1755-0998.12438

Additionally, please cite the Dryad data package:

Cheng T, Xu C, Lei L, Li C, Zhang Y, Zhou S (2015) Data from: Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.p3ks4
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